Merge branch 'cumc:main' into main

cumc · Sep 27, 2024 · e8f653c · e8f653c
2 parents e793264 + 0c7b146
commit e8f653c
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diff --git a/code/mnm_analysis/multivariate_multigene_fine_mapping_vignette.ipynb b/code/mnm_analysis/multivariate_multigene_fine_mapping_vignette.ipynb
@@ -81,9 +81,9 @@
     "\n",
     "`--skip-analysis-pip-cutoff`: A number of the pip cutoff. \n",
     "\n",
-    "`--coverage`:\n",
+    "`--coverage`\n",
     "\n",
-    "`--maf`:\n",
+    "`--maf`\n",
     "\n",
     "`--pheno_id_map_file`: A file containing IDs and genes.\n",
     "For example:\n",
@@ -94,13 +94,13 @@
     "chr20:50936262:50942031:clu_44490_-:ENSG00000000419     ENSG00000000419\n",
     "```\n",
     "\n",
-    "`--prior-canonical-matrices`:\n",
+    "`--prior-canonical-matrices`\n",
     "\n",
-    "`--save-data`:\n",
+    "`--save-data`: whether to save intermediate data or not\n",
     "\n",
-    "`--twas-cv-folds`:\n",
+    "`--twas-cv-folds`: Perform K folds valiation CV for TWAS. Set this to zero to skip\n",
     "\n",
-    "`--trans-analysis`:\n",
+    "`--trans-analysis`: Include this if doing trans-analysis (not using phenotypic coordinate information)\n",
     "\n",
     "`--region-name`: if you only wish to analyze one region, then include the ID of a region found in the `customized-association-windows` file\n",
     "\n",
@@ -120,7 +120,7 @@
    "id": "53488842-fb88-477e-9b44-5660b0c39ebb",
    "metadata": {},
    "source": [
-    "1. Run mnm_gene"
+    "1. Run mnm_genes"
    ]
   },
   {
@@ -144,14 +144,14 @@
    "id": "4f43b0d7-c393-4a89-8ac6-9f18f6eda94d",
    "metadata": {},
    "source": [
-    "sos run $PATH/mnm_regression.ipynb mnm_genes \\\n",
-    "    --name ROSMAP_Mic_DeJager_eQTL \\\n",
-    "    --genoFile $PATH/ROSMAP_NIA_WGS.leftnorm.bcftools_qc.plink_qc.22.bed \\\n",
-    "    --phenoFile $PATH/snuc_pseudo_bulk.Mic.mega.normalized.log2cpm.region_list.txt \\\n",
-    "    --covFile $PATH/snuc_pseudo_bulk.Mic.mega.normalized.log2cpm.rosmap_cov.ROSMAP_NIA_WGS.leftnorm.bcftools_qc.plink_qc.snuc_pseudo_bulk_mega.related.plink_qc.extracted.pca.projected.Marchenko_PC.gz \\\n",
-    "    --customized-association-windows $PATH/TADB_sliding_window.bed \\\n",
-    "    --phenotype-names Mic_DeJager_eQTL \\\n",
-    "    --max-cv-variants 5000 --ld_reference_meta_file $PATH/ld_meta_file.tsv \\\n",
+    "sos run $PATH/protocol/pipeline/mnm_regression.ipynb mnm_genes \\\n",
+    "    --name ROSMAP_Ast_DeJager_eQTL \\\n",
+    "    --genoFile $PATH/ROSMAP_NIA_WGS.leftnorm.bcftools_qc.plink_qc.11.bed \\\n",
+    "    --phenoFile $PATH/snuc_pseudo_bulk.Ast.mega.normalized.log2cpm.region_list.txt \\\n",
+    "    --covFile $PATH/snuc_pseudo_bulk.Ast.mega.normalized.log2cpm.rosmap_cov.ROSMAP_NIA_WGS.leftnorm.bcftools_qc.plink_qc.snuc_pseudo_bulk_mega.related.plink_qc.extracted.pca.projected.Marchenko_PC.gz \\\n",
+    "    --customized-association-windows $PATH/windows/TADB_sliding_window.bed \\\n",
+    "    --phenotype-names Ast_DeJager_eQTL \\\n",
+    "    --max-cv-variants 5000 --ld_reference_meta_file $PATH/ldref/ld_meta_file.tsv \\\n",
     "    --independent_variant_list $PATH/ld_pruned_variants.txt.gz \\\n",
     "    --fine_mapping_meta $PATH/Fungen_xQTL.cis_results_db.new.tsv \\\n",
     "    --phenoIDFile $PATH/phenoIDFile_cis_extended_region.bed \\\n",
@@ -163,8 +163,8 @@
     "    --save-data \\\n",
     "    --twas-cv-folds 0 \\\n",
     "    --trans-analysis \\\n",
-    "    --region-name chr22_0_22700015 \\ \n",
-    "    --cwd /home/frankgrenn/output/ -s force"
+    "    --region-name chr11_77324757_86627922 \\ \n",
+    "    --cwd $PATH/output/ -s force"
    ]
   },
   {
@@ -180,12 +180,31 @@
    "id": "199a2637-cc0c-4aff-b4ea-a2546936f073",
    "metadata": {},
    "source": [
-    "`ROSMAP_Mic_DeJager_eQTL.chr22_0_22700015.multigene_bvrs.rds`:\n",
-    "\n",
-    "`ROSMAP_Mic_DeJager_eQTL.chr22_0_22700015.multigene_data.rds`:(from the --save-data argument)\n",
+    "`ROSMAP_Ast_DeJager_eQTL.chr11_77324757_86627922.multigene_bvrs.rds`:\n",
+    "* for each region name, includes:\n",
+    "1. mrmash_fitted\n",
+    "2. reweighted_mixture_prior\n",
+    "3. reweighted_mixture_prior_cv\n",
+    "4. mvsusie_fitted\n",
+    "5. variant_names\n",
+    "6. analysis_script\n",
+    "7. other_quantitites\n",
+    "8. analysis_script\n",
+    "9. top_loci\n",
+    "10. susie_result_trimmed\n",
+    "11. total_time_elapsed\n",
+    "12. region_info\n",
+    "\n",
+    "`ROSMAP_Ast_DeJager_eQTL.chr11_77324757_86627922.multigene_data.rds`:(from the --save-data argument)\n",
     "* see [pecotmr code](https://github.com/cumc/pecotmr/blob/68d87ca1d0a059022bf4e55339621cbddc8993cc/R/file_utils.R#L461) for description \n",
     "\n",
-    "`ROSMAP_Mic_DeJager_eQTL.chr22_0_22700015.multigene_twas_weights.rds`:\n"
+    "`ROSMAP_Ast_DeJager_eQTL.chr11_77324757_86627922.multigene_twas_weights.rds`:\n",
+    "* for each region name and for each gene within that region, includes:\n",
+    "1. twas_weights - from mrmash and mvsusie\n",
+    "2. twas_predictions - from mrmash and mvsusie\n",
+    "3. variant_names\n",
+    "4. total_time_elapsed\n",
+    "5. region_info"
    ]
   },
   {

diff --git a/code/pecotmr_integration/ctwas.ipynb b/code/pecotmr_integration/ctwas.ipynb